Extrusions causing problems in edit mode
First, the "grainy black texture" is z-fighting. Some where you have overlapping faces.

The automatic extrusions on the x-axis is from the normal value of the face you are extruding from. You can after hitting E press Z and that will disable the guide along the normal.

I'm not sure what you mean by "it doesn't allow me to extrude planes into 3-D shapes." If you select a face in face select mode(change the selection mode with CtrlTab) then press E you will have a 3D shape.